import jalview.datamodel.SequenceI;
import jalview.renderer.ScaleRenderer;
import jalview.renderer.ScaleRenderer.ScaleMark;
-import jalview.util.Comparison;
import jalview.viewmodel.ViewportListenerI;
import jalview.viewmodel.ViewportRanges;
import javax.swing.JComponent;
/**
- * The Swing component on which the alignment sequences, and annotations (if
- * shown), are drawn. This includes scales above, left and right (if shown) in
- * Wrapped mode, but not the scale above in Unwrapped mode.
+ * DOCUMENT ME!
*
+ * @author $author$
+ * @version $Revision$
*/
public class SeqCanvas extends JComponent implements ViewportListenerI
{
- private static final String ZEROS = "0000000000";
+ private static String ZEROS = "0000000000";
final FeatureRenderer fr;
- BufferedImage img;
-
- AlignViewport av;
+ final SequenceRenderer seqRdr;
- int cursorX = 0;
+ BufferedImage img;
- int cursorY = 0;
+ Graphics2D gg;
- private final SequenceRenderer seqRdr;
+ AlignViewport av;
- private boolean fastPaint = false;
+ boolean fastPaint = false;
- private boolean fastpainting = false;
+ int labelWidthWest;
- private AnnotationPanel annotations;
+ int labelWidthEast;
- /*
- * measurements for drawing a wrapped alignment
- */
- private int labelWidthEast; // label right width in pixels if shown
+ int cursorX = 0;
- private int labelWidthWest; // label left width in pixels if shown
+ int cursorY = 0;
- private int wrappedSpaceAboveAlignment; // gap between widths
+ int charHeight = 0;
- private int wrappedRepeatHeightPx; // height in pixels of wrapped width
+ int charWidth = 0;
- private int wrappedVisibleWidths; // number of wrapped widths displayed
+ boolean fastpainting = false;
- private Graphics2D gg;
+ AnnotationPanel annotations;
/**
* Creates a new SeqCanvas object.
*
- * @param ap
+ * @param av
+ * DOCUMENT ME!
*/
public SeqCanvas(AlignmentPanel ap)
{
this.av = ap.av;
+ updateViewport();
fr = new FeatureRenderer(ap);
seqRdr = new SequenceRenderer(av);
setLayout(new BorderLayout());
return fr;
}
+ private void updateViewport()
+ {
+ charHeight = av.getCharHeight();
+ charWidth = av.getCharWidth();
+ }
+
/**
- * Draws the scale above a region of a wrapped alignment, consisting of a
- * column number every major interval (10 columns).
+ * DOCUMENT ME!
*
* @param g
- * the graphics context to draw on, positioned at the start (bottom
- * left) of the line on which to draw any scale marks
+ * DOCUMENT ME!
* @param startx
- * start alignment column (0..)
+ * DOCUMENT ME!
* @param endx
- * end alignment column (0..)
+ * DOCUMENT ME!
* @param ypos
- * y offset to draw at
+ * DOCUMENT ME!
*/
private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
{
- int charHeight = av.getCharHeight();
- int charWidth = av.getCharWidth();
-
- /*
- * white fill the scale space (for the fastPaint case)
- */
- g.setColor(Color.white);
- g.fillRect(0, ypos - charHeight - charHeight / 2, getWidth(),
- charHeight * 3 / 2 + 2);
- g.setColor(Color.black);
-
- List<ScaleMark> marks = new ScaleRenderer().calculateMarks(av, startx,
- endx);
- for (ScaleMark mark : marks)
+ updateViewport();
+ for (ScaleMark mark : new ScaleRenderer().calculateMarks(av, startx,
+ endx))
{
int mpos = mark.column; // (i - startx - 1)
if (mpos < 0)
{
g.drawString(mstring, mpos * charWidth, ypos - (charHeight / 2));
}
-
- /*
- * draw a tick mark below the column number, centred on the column;
- * height of tick mark is 4 pixels less than half a character
- */
- int xpos = (mpos * charWidth) + (charWidth / 2);
- g.drawLine(xpos, (ypos + 2) - (charHeight / 2), xpos, ypos - 2);
+ g.drawLine((mpos * charWidth) + (charWidth / 2),
+ (ypos + 2) - (charHeight / 2),
+ (mpos * charWidth) + (charWidth / 2), ypos - 2);
}
}
}
/**
- * Draw the scale to the left or right of a wrapped alignment
+ * DOCUMENT ME!
*
* @param g
- * graphics context, positioned at the start of the scale to be drawn
+ * DOCUMENT ME!
* @param startx
- * first column of wrapped width (0.. excluding any hidden columns)
+ * DOCUMENT ME!
* @param endx
- * last column of wrapped width (0.. excluding any hidden columns)
+ * DOCUMENT ME!
* @param ypos
- * vertical offset at which to begin the scale
- * @param left
- * if true, scale is left of residues, if false, scale is right
+ * DOCUMENT ME!
*/
- void drawVerticalScale(Graphics g, final int startx, final int endx,
- final int ypos, final boolean left)
+ void drawWestScale(Graphics g, int startx, int endx, int ypos)
{
- int charHeight = av.getCharHeight();
- int charWidth = av.getCharWidth();
+ FontMetrics fm = getFontMetrics(av.getFont());
+ ypos += charHeight;
- int yPos = ypos + charHeight;
- int startX = startx;
- int endX = endx;
+ if (av.hasHiddenColumns())
+ {
+ startx = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(startx);
+ endx = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(endx);
+ }
+ int maxwidth = av.getAlignment().getWidth();
if (av.hasHiddenColumns())
{
- HiddenColumns hiddenColumns = av.getAlignment().getHiddenColumns();
- startX = hiddenColumns.adjustForHiddenColumns(startx);
- endX = hiddenColumns.adjustForHiddenColumns(endx);
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth) - 1;
}
- FontMetrics fm = getFontMetrics(av.getFont());
+ // WEST SCALE
for (int i = 0; i < av.getAlignment().getHeight(); i++)
{
SequenceI seq = av.getAlignment().getSequenceAt(i);
-
- /*
- * find sequence position of first non-gapped position -
- * to the right if scale left, to the left if scale right
- */
- int index = left ? startX : endX;
+ int index = startx;
int value = -1;
- while (index >= startX && index <= endX)
+
+ while (index < endx)
{
- if (!Comparison.isGap(seq.getCharAt(index)))
- {
- value = seq.findPosition(index);
- break;
- }
- if (left)
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
{
index++;
+
+ continue;
}
- else
+
+ value = av.getAlignment().getSequenceAt(i).findPosition(index);
+
+ break;
+ }
+
+ if (value != -1)
+ {
+ int x = labelWidthWest - fm.stringWidth(String.valueOf(value))
+ - charWidth / 2;
+ g.drawString(value + "", x,
+ (ypos + (i * charHeight)) - (charHeight / 5));
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
+ * @param startx
+ * DOCUMENT ME!
+ * @param endx
+ * DOCUMENT ME!
+ * @param ypos
+ * DOCUMENT ME!
+ */
+ void drawEastScale(Graphics g, int startx, int endx, int ypos)
+ {
+ ypos += charHeight;
+
+ if (av.hasHiddenColumns())
+ {
+ endx = av.getAlignment().getHiddenColumns()
+ .adjustForHiddenColumns(endx);
+ }
+
+ SequenceI seq;
+ // EAST SCALE
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
+ {
+ seq = av.getAlignment().getSequenceAt(i);
+ int index = endx;
+ int value = -1;
+
+ while (index > startx)
+ {
+ if (jalview.util.Comparison.isGap(seq.getCharAt(index)))
{
index--;
+
+ continue;
}
- }
- /*
- * white fill the space for the scale
- */
- g.setColor(Color.white);
- int y = (yPos + (i * charHeight)) - (charHeight / 5);
- // fillRect origin is top left of rectangle
- g.fillRect(0, y - charHeight, left ? labelWidthWest : labelWidthEast,
- charHeight + 1);
+ value = seq.findPosition(index);
+
+ break;
+ }
if (value != -1)
{
- /*
- * draw scale value, right justified within its width less half a
- * character width padding on the right
- */
- int labelSpace = left ? labelWidthWest : labelWidthEast;
- labelSpace -= charWidth / 2; // leave space to the right
- String valueAsString = String.valueOf(value);
- int labelLength = fm.stringWidth(valueAsString);
- int xOffset = labelSpace - labelLength;
- g.setColor(Color.black);
- g.drawString(valueAsString, xOffset, y);
+ g.drawString(String.valueOf(value), 0,
+ (ypos + (i * charHeight)) - (charHeight / 5));
}
}
}
+
/**
- * Does a fast paint of an alignment in response to a scroll. Most of the
- * visible region is simply copied and shifted, and then any newly visible
- * columns or rows are drawn. The scroll may be horizontal or vertical, but
- * not both at once. Scrolling may be the result of
- * <ul>
- * <li>dragging a scroll bar</li>
- * <li>clicking in the scroll bar</li>
- * <li>scrolling by trackpad, middle mouse button, or other device</li>
- * <li>by moving the box in the Overview window</li>
- * <li>programmatically to make a highlighted position visible</li>
- * </ul>
+ * need to make this thread safe move alignment rendering in response to
+ * slider adjustment
*
* @param horizontal
- * columns to shift right (positive) or left (negative)
+ * shift along
* @param vertical
- * rows to shift down (positive) or up (negative)
+ * shift up or down in repaint
*/
public void fastPaint(int horizontal, int vertical)
{
}
fastpainting = true;
fastPaint = true;
+ updateViewport();
- try
- {
- int charHeight = av.getCharHeight();
- int charWidth = av.getCharWidth();
-
- ViewportRanges ranges = av.getRanges();
- int startRes = ranges.getStartRes();
- int endRes = ranges.getEndRes();
- int startSeq = ranges.getStartSeq();
- int endSeq = ranges.getEndSeq();
- int transX = 0;
- int transY = 0;
+ ViewportRanges ranges = av.getRanges();
+ int startRes = ranges.getStartRes();
+ int endRes = ranges.getEndRes();
+ int startSeq = ranges.getStartSeq();
+ int endSeq = ranges.getEndSeq();
+ int transX = 0;
+ int transY = 0;
gg.copyArea(horizontal * charWidth, vertical * charHeight,
img.getWidth(), img.getHeight(), -horizontal * charWidth,
gg.translate(-transX, -transY);
repaint();
- } finally
- {
- fastpainting = false;
- }
+ fastpainting = false;
}
@Override
public void paintComponent(Graphics g)
{
- super.paintComponent(g);
-
- int charHeight = av.getCharHeight();
- int charWidth = av.getCharWidth();
+ super.paintComponent(g);
+
+ updateViewport();
ViewportRanges ranges = av.getRanges();
g.drawImage(lcimg, 0, 0, this);
}
}
-
+
/**
* Draw an alignment panel for printing
*
{
BufferedImage lcimg = null;
- int charWidth = av.getCharWidth();
- int charHeight = av.getCharHeight();
-
int width = getWidth();
int height = getHeight();
*/
public int getWrappedCanvasWidth(int canvasWidth)
{
- int charWidth = av.getCharWidth();
-
FontMetrics fm = getFontMetrics(av.getFont());
- int labelWidth = 0;
-
- if (av.getScaleRightWrapped() || av.getScaleLeftWrapped())
+ labelWidthEast = 0;
+ labelWidthWest = 0;
+
+ if (av.getScaleRightWrapped())
{
- labelWidth = getLabelWidth(fm);
+ labelWidthEast = getLabelWidth(fm);
}
- labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0;
-
- labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0;
+ if (av.getScaleLeftWrapped())
+ {
+ labelWidthWest = labelWidthEast > 0 ? labelWidthEast
+ : getLabelWidth(fm);
+ }
return (canvasWidth - labelWidthEast - labelWidthWest) / charWidth;
}
/**
- * Returns a pixel width sufficient to show the largest sequence coordinate
- * (end position) in the alignment, calculated as the FontMetrics width of
- * zeroes "0000000" limited to the number of decimal digits to be shown (3 for
- * 1-10, 4 for 11-99 etc). One character width is added to this, to allow for
- * half a character width space on either side.
+ * Returns a pixel width suitable for showing the largest sequence coordinate
+ * (end position) in the alignment. Returns 2 plus the number of decimal
+ * digits to be shown (3 for 1-10, 4 for 11-99 etc).
*
* @param fm
* @return
maxWidth = Math.max(maxWidth, alignment.getSequenceAt(i).getEnd());
}
- int length = 0;
+ int length = 2;
for (int i = maxWidth; i > 0; i /= 10)
{
length++;
}
- return fm.stringWidth(ZEROS.substring(0, length)) + av.getCharWidth();
+ return fm.stringWidth(ZEROS.substring(0, length));
}
/**
- * Draws as many widths of a wrapped alignment as can fit in the visible
- * window
+ * DOCUMENT ME!
*
* @param g
+ * DOCUMENT ME!
* @param canvasWidth
- * available width in pixels
+ * DOCUMENT ME!
* @param canvasHeight
- * available height in pixels
- * @param startColumn
- * the first column (0...) of the alignment to draw
- */
- public void drawWrappedPanel(Graphics g, int canvasWidth,
- int canvasHeight, final int startColumn)
- {
- int wrappedWidthInResidues = calculateWrappedGeometry(canvasWidth,
- canvasHeight);
-
- av.setWrappedWidth(wrappedWidthInResidues);
-
- ViewportRanges ranges = av.getRanges();
- ranges.setViewportStartAndWidth(startColumn, wrappedWidthInResidues);
-
- /*
- * draw one width at a time (including any scales or annotation shown),
- * until we have run out of either alignment or vertical space available
- */
- int ypos = wrappedSpaceAboveAlignment;
- int maxWidth = ranges.getVisibleAlignmentWidth();
-
- int start = startColumn;
- int currentWidth = 0;
- while ((currentWidth < wrappedVisibleWidths) && (start < maxWidth))
- {
- int endColumn = Math
- .min(maxWidth, start + wrappedWidthInResidues - 1);
- drawWrappedWidth(g, ypos, start, endColumn, canvasHeight);
- ypos += wrappedRepeatHeightPx;
- start += wrappedWidthInResidues;
- currentWidth++;
- }
-
- drawWrappedDecorators(g, startColumn);
- }
-
- /**
- * Calculates and saves values needed when rendering a wrapped alignment.
- * These depend on many factors, including
- * <ul>
- * <li>canvas width and height</li>
- * <li>number of visible sequences, and height of annotations if shown</li>
- * <li>font and character width</li>
- * <li>whether scales are shown left, right or above the alignment</li>
- * </ul>
- *
- * @param canvasWidth
- * @param canvasHeight
- * @return the number of residue columns in each width
+ * DOCUMENT ME!
+ * @param startRes
+ * DOCUMENT ME!
*/
- protected int calculateWrappedGeometry(int canvasWidth, int canvasHeight)
+ private void drawWrappedPanel(Graphics g, int canvasWidth,
+ int canvasHeight, int startRes)
{
- int charHeight = av.getCharHeight();
-
- /*
- * vertical space in pixels between wrapped widths of alignment
- * - one character height, or two if scale above is drawn
- */
- wrappedSpaceAboveAlignment = charHeight
- * (av.getScaleAboveWrapped() ? 2 : 1);
-
- /*
- * height in pixels of the wrapped widths
- */
- wrappedRepeatHeightPx = wrappedSpaceAboveAlignment;
- // add sequences
- wrappedRepeatHeightPx += av.getRanges().getViewportHeight()
- * charHeight;
- // add annotations panel height if shown
- wrappedRepeatHeightPx += getAnnotationHeight();
+ updateViewport();
+ AlignmentI al = av.getAlignment();
- /*
- * number of visible widths (the last one may be part height),
- * ensuring a part height includes at least one sequence
- */
- ViewportRanges ranges = av.getRanges();
- wrappedVisibleWidths = canvasHeight / wrappedRepeatHeightPx;
- int remainder = canvasHeight % wrappedRepeatHeightPx;
- if (remainder >= (wrappedSpaceAboveAlignment + charHeight))
+ int labelWidth = 0;
+ if (av.getScaleRightWrapped() || av.getScaleLeftWrapped())
{
- wrappedVisibleWidths++;
+ FontMetrics fm = getFontMetrics(av.getFont());
+ labelWidth = getLabelWidth(fm);
}
- /*
- * compute width in residues; this also sets East and West label widths
- */
- int wrappedWidthInResidues = getWrappedCanvasWidth(canvasWidth);
+ labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0;
+ labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0;
- /*
- * limit visibleWidths to not exceed width of alignment
- */
- int xMax = ranges.getVisibleAlignmentWidth();
- int startToEnd = xMax - ranges.getStartRes();
- int maxWidths = startToEnd / wrappedWidthInResidues;
- if (startToEnd % wrappedWidthInResidues > 0)
+ int hgap = charHeight;
+ if (av.getScaleAboveWrapped())
{
- maxWidths++;
+ hgap += charHeight;
}
- wrappedVisibleWidths = Math.min(wrappedVisibleWidths, maxWidths);
-
- return wrappedWidthInResidues;
- }
- /**
- * Draws one width of a wrapped alignment, including sequences and
- * annnotations, if shown, but not scales or hidden column markers
- *
- * @param g
- * @param ypos
- * @param startColumn
- * @param endColumn
- * @param canvasHeight
- */
- protected void drawWrappedWidth(Graphics g, int ypos, int startColumn,
- int endColumn, int canvasHeight)
- {
- ViewportRanges ranges = av.getRanges();
- int viewportWidth = ranges.getViewportWidth();
+ int cWidth = (canvasWidth - labelWidthEast - labelWidthWest) / charWidth;
+ int cHeight = av.getAlignment().getHeight() * charHeight;
- int endx = Math.min(startColumn + viewportWidth - 1, endColumn);
+ av.setWrappedWidth(cWidth);
- /*
- * move right before drawing by the width of the scale left (if any)
- * plus column offset from left margin (usually zero, but may be non-zero
- * when fast painting is drawing just a few columns)
- */
- int charWidth = av.getCharWidth();
- int xOffset = labelWidthWest
- + ((startColumn - ranges.getStartRes()) % viewportWidth)
- * charWidth;
- g.translate(xOffset, 0);
+ av.getRanges().setViewportStartAndWidth(startRes, cWidth);
- // When printing we have an extra clipped region,
- // the Printable page which we need to account for here
- Shape clip = g.getClip();
+ int endx;
+ int ypos = hgap;
+ int maxwidth = av.getAlignment().getWidth();
- if (clip == null)
- {
- g.setClip(0, 0, viewportWidth * charWidth, canvasHeight);
- }
- else
+ if (av.hasHiddenColumns())
{
- g.setClip(0, (int) clip.getBounds().getY(),
- viewportWidth * charWidth, (int) clip.getBounds().getHeight());
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth);
}
- /*
- * white fill the region to be drawn (so incremental fast paint doesn't
- * scribble over an existing image)
- */
- gg.setColor(Color.white);
- gg.fillRect(0, ypos, (endx - startColumn + 1) * charWidth,
- wrappedRepeatHeightPx);
-
- drawPanel(g, startColumn, endx, 0, av.getAlignment().getHeight() - 1,
- ypos);
-
- int cHeight = av.getAlignment().getHeight() * av.getCharHeight();
+ int annotationHeight = getAnnotationHeight();
- if (av.isShowAnnotation())
+ while ((ypos <= canvasHeight) && (startRes < maxwidth))
{
- g.translate(0, cHeight + ypos + 3);
- if (annotations == null)
+ endx = startRes + cWidth - 1;
+
+ if (endx > maxwidth)
{
- annotations = new AnnotationPanel(av);
+ endx = maxwidth;
}
- annotations.renderer.drawComponent(annotations, av, g, -1,
- startColumn, endx + 1);
- g.translate(0, -cHeight - ypos - 3);
- }
- g.setClip(clip);
- g.translate(-xOffset, 0);
- }
-
- /**
- * Draws scales left, right and above (if shown), and any hidden column
- * markers, on all widths of the wrapped alignment
- *
- * @param g
- * @param startColumn
- */
- protected void drawWrappedDecorators(Graphics g, final int startColumn)
- {
- int charWidth = av.getCharWidth();
-
- g.setFont(av.getFont());
- g.setColor(Color.black);
-
- int ypos = wrappedSpaceAboveAlignment;
- ViewportRanges ranges = av.getRanges();
- int viewportWidth = ranges.getViewportWidth();
- int maxWidth = ranges.getVisibleAlignmentWidth();
- int widthsDrawn = 0;
- int startCol = startColumn;
-
- while (widthsDrawn < wrappedVisibleWidths)
- {
- int endColumn = Math.min(maxWidth, startCol + viewportWidth - 1);
+ g.setFont(av.getFont());
+ g.setColor(Color.black);
if (av.getScaleLeftWrapped())
{
- drawVerticalScale(g, startCol, endColumn - 1, ypos, true);
+ drawWestScale(g, startRes, endx, ypos);
}
if (av.getScaleRightWrapped())
{
- int x = labelWidthWest + viewportWidth * charWidth;
- g.translate(x, 0);
- drawVerticalScale(g, startCol, endColumn, ypos, false);
- g.translate(-x, 0);
+ g.translate(canvasWidth - labelWidthEast, 0);
+ drawEastScale(g, startRes, endx, ypos);
+ g.translate(-(canvasWidth - labelWidthEast), 0);
}
- /*
- * white fill region of scale above and hidden column markers
- * (to support incremental fast paint of image)
- */
- g.translate(labelWidthWest, 0);
- g.setColor(Color.white);
- g.fillRect(0, ypos - wrappedSpaceAboveAlignment, viewportWidth
- * charWidth + labelWidthWest, wrappedSpaceAboveAlignment);
- g.setColor(Color.black);
- g.translate(-labelWidthWest, 0);
-
g.translate(labelWidthWest, 0);
if (av.getScaleAboveWrapped())
{
- drawNorthScale(g, startCol, endColumn, ypos);
+ drawNorthScale(g, startRes, endx, ypos);
}
if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
{
- drawHiddenColumnMarkers(g, ypos, startCol, endColumn);
- }
+ g.setColor(Color.blue);
+ int res;
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ List<Integer> positions = hidden.findHiddenRegionPositions();
+ for (int pos : positions)
+ {
+ res = pos - startRes;
- g.translate(-labelWidthWest, 0);
+ if (res < 0 || res > endx - startRes)
+ {
+ continue;
+ }
- ypos += wrappedRepeatHeightPx;
- startCol += viewportWidth;
- widthsDrawn++;
- }
- }
+ gg.fillPolygon(
+ new int[]
+ { res * charWidth - charHeight / 4,
+ res * charWidth + charHeight / 4, res * charWidth },
+ new int[]
+ { ypos - (charHeight / 2), ypos - (charHeight / 2),
+ ypos - (charHeight / 2) + 8 },
+ 3);
- /**
- * Draws markers (triangles) above hidden column positions between startColumn
- * and endColumn.
- *
- * @param g
- * @param ypos
- * @param startColumn
- * @param endColumn
- */
- protected void drawHiddenColumnMarkers(Graphics g, int ypos,
- int startColumn, int endColumn)
- {
- int charHeight = av.getCharHeight();
- int charWidth = av.getCharWidth();
+ }
+ }
- g.setColor(Color.blue);
- HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- List<Integer> positions = hidden.findHiddenRegionPositions();
- for (int pos : positions)
- {
- int res = pos - startColumn;
+ // When printing we have an extra clipped region,
+ // the Printable page which we need to account for here
+ Shape clip = g.getClip();
- if (res < 0 || res > endColumn - startColumn + 1)
+ if (clip == null)
{
- continue;
+ g.setClip(0, 0, cWidth * charWidth, canvasHeight);
+ }
+ else
+ {
+ g.setClip(0, (int) clip.getBounds().getY(), cWidth * charWidth,
+ (int) clip.getBounds().getHeight());
}
- /*
- * draw a downward-pointing triangle at the hidden columns location
- * (before the following visible column)
- */
- int xMiddle = res * charWidth;
- int[] xPoints = new int[] { xMiddle - charHeight / 4,
- xMiddle + charHeight / 4, xMiddle };
- int yTop = ypos - (charHeight / 2);
- int[] yPoints = new int[] { yTop, yTop, yTop + 8 };
- g.fillPolygon(xPoints, yPoints, 3);
+ drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos);
+
+ if (av.isShowAnnotation())
+ {
+ g.translate(0, cHeight + ypos + 3);
+ if (annotations == null)
+ {
+ annotations = new AnnotationPanel(av);
+ }
+
+ annotations.renderer.drawComponent(annotations, av, g, -1, startRes,
+ endx + 1);
+ g.translate(0, -cHeight - ypos - 3);
+ }
+ g.setClip(clip);
+ g.translate(-labelWidthWest, 0);
+
+ ypos += cHeight + annotationHeight + hgap;
+
+ startRes += cWidth;
}
}
int canvasWidth,
int canvasHeight, int startRes)
{
- int charHeight = av.getCharHeight();
- int charWidth = av.getCharWidth();
-
// height gap above each panel
int hgap = charHeight;
if (av.getScaleAboveWrapped())
* marker.
*
* @param g1
- * the graphics context, positioned at the first residue to be drawn
+ * Graphics object to draw with
* @param startRes
- * offset of the first column to draw (0..)
+ * offset of the first column in the visible region (0..)
* @param endRes
- * offset of the last column to draw (0..)
+ * offset of the last column in the visible region (0..)
* @param startSeq
- * offset of the first sequence to draw (0..)
+ * offset of the first sequence in the visible region (0..)
* @param endSeq
- * offset of the last sequence to draw (0..)
+ * offset of the last sequence in the visible region (0..)
* @param yOffset
* vertical offset at which to draw (for wrapped alignments)
*/
public void drawPanel(Graphics g1, final int startRes, final int endRes,
final int startSeq, final int endSeq, final int yOffset)
{
- int charHeight = av.getCharHeight();
- int charWidth = av.getCharWidth();
-
+ updateViewport();
if (!av.hasHiddenColumns())
{
draw(g1, startRes, endRes, startSeq, endSeq, yOffset);
private void draw(Graphics g, int startRes, int endRes, int startSeq,
int endSeq, int offset)
{
- int charHeight = av.getCharHeight();
- int charWidth = av.getCharWidth();
-
g.setFont(av.getFont());
seqRdr.prepare(g, av.isRenderGaps());
private void drawUnwrappedSelection(Graphics2D g, SequenceGroup group,
int startRes, int endRes, int startSeq, int endSeq, int offset)
{
- int charWidth = av.getCharWidth();
-
if (!av.hasHiddenColumns())
{
drawPartialGroupOutline(g, group, startRes, endRes, startSeq, endSeq,
int startRes, int endRes, int startSeq, int endSeq,
int verticalOffset)
{
- int charHeight = av.getCharHeight();
- int charWidth = av.getCharWidth();
-
int visWidth = (endRes - startRes + 1) * charWidth;
int oldY = -1;
return false;
}
boolean wrapped = av.getWrapAlignment();
+
try
{
fastPaint = !noFastPaint;
fastpainting = fastPaint;
+ updateViewport();
+
/*
* to avoid redrawing the whole visible region, we instead
* redraw just the minimal regions to remove previous highlights
return matchFound;
}
+
@Override
public void propertyChange(PropertyChangeEvent evt)
{
{
fastPaint = true;
repaint();
- return;
}
-
- int scrollX = 0;
- if (eventName.equals(ViewportRanges.STARTRES))
+ else if (av.getWrapAlignment())
{
- // Make sure we're not trying to draw a panel
- // larger than the visible window
- ViewportRanges vpRanges = av.getRanges();
- scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
- int range = vpRanges.getViewportWidth();
- if (scrollX > range)
- {
- scrollX = range;
- }
- else if (scrollX < -range)
+ if (eventName.equals(ViewportRanges.STARTRES)
+ || eventName.equals(ViewportRanges.STARTRESANDSEQ))
{
- scrollX = -range;
+ repaint();
}
}
-
- // Both scrolling and resizing change viewport ranges: scrolling changes
- // both start and end points, but resize only changes end values.
- // Here we only want to fastpaint on a scroll, with resize using a normal
- // paint, so scroll events are identified as changes to the horizontal or
- // vertical start value.
-
- // scroll - startres and endres both change
- if (eventName.equals(ViewportRanges.STARTRES))
+ else
{
- if (av.getWrapAlignment())
- {
- fastPaintWrapped(scrollX);
- }
- else
+ int scrollX = 0;
+ if (eventName.equals(ViewportRanges.STARTRES)
+ || eventName.equals(ViewportRanges.STARTRESANDSEQ))
{
- fastPaint(scrollX, 0);
- }
- }
- else if (eventName.equals(ViewportRanges.STARTSEQ))
- {
- // scroll
- fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
- }
- }
-
- /**
- * Does a minimal update of the image for a scroll movement. This method
- * handles scroll movements of up to one width of the wrapped alignment (one
- * click in the vertical scrollbar). Larger movements (for example after a
- * scroll to highlight a mapped position) trigger a full redraw instead.
- *
- * @param scrollX
- * number of positions scrolled (right if positive, left if negative)
- */
- protected void fastPaintWrapped(int scrollX)
- {
- ViewportRanges ranges = av.getRanges();
-
- if (Math.abs(scrollX) > ranges.getViewportWidth())
- {
- /*
- * shift of more than one view width is
- * overcomplicated to handle in this method
- */
- fastPaint = false;
- repaint();
- return;
- }
-
- if (fastpainting || gg == null)
- {
- return;
- }
-
- fastPaint = true;
- fastpainting = true;
-
- try
- {
- calculateWrappedGeometry(getWidth(), getHeight());
-
- /*
- * relocate the regions of the alignment that are still visible
- */
- shiftWrappedAlignment(-scrollX);
+ // Make sure we're not trying to draw a panel
+ // larger than the visible window
+ if (eventName.equals(ViewportRanges.STARTRES))
+ {
+ scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
+ }
+ else
+ {
+ scrollX = ((int[]) evt.getNewValue())[0]
+ - ((int[]) evt.getOldValue())[0];
+ }
+ ViewportRanges vpRanges = av.getRanges();
- /*
- * add new columns (sequence, annotation)
- * - at top left if scrollX < 0
- * - at right of last two widths if scrollX > 0
- */
- if (scrollX < 0)
- {
- int startRes = ranges.getStartRes();
- drawWrappedWidth(gg, wrappedSpaceAboveAlignment, startRes, startRes
- - scrollX - 1, getHeight());
+ int range = vpRanges.getEndRes() - vpRanges.getStartRes();
+ if (scrollX > range)
+ {
+ scrollX = range;
+ }
+ else if (scrollX < -range)
+ {
+ scrollX = -range;
+ }
}
- else
+
+ // Both scrolling and resizing change viewport ranges: scrolling changes
+ // both start and end points, but resize only changes end values.
+ // Here we only want to fastpaint on a scroll, with resize using a normal
+ // paint, so scroll events are identified as changes to the horizontal or
+ // vertical start value.
+ if (eventName.equals(ViewportRanges.STARTRES))
{
- fastPaintWrappedAddRight(scrollX);
+ // scroll - startres and endres both change
+ fastPaint(scrollX, 0);
}
-
- /*
- * draw all scales (if shown) and hidden column markers
- */
- drawWrappedDecorators(gg, ranges.getStartRes());
-
- repaint();
- } finally
- {
- fastpainting = false;
- }
- }
-
- /**
- * Draws the specified number of columns at the 'end' (bottom right) of a
- * wrapped alignment view, including sequences and annotations if shown, but
- * not scales. Also draws the same number of columns at the right hand end of
- * the second last width shown, if the last width is not full height (so
- * cannot simply be copied from the graphics image).
- *
- * @param columns
- */
- protected void fastPaintWrappedAddRight(int columns)
- {
- if (columns == 0)
- {
- return;
- }
-
- ViewportRanges ranges = av.getRanges();
- int viewportWidth = ranges.getViewportWidth();
- int charWidth = av.getCharWidth();
-
- /**
- * draw full height alignment in the second last row, last columns, if the
- * last row was not full height
- */
- int visibleWidths = wrappedVisibleWidths;
- int canvasHeight = getHeight();
- boolean lastWidthPartHeight = (wrappedVisibleWidths * wrappedRepeatHeightPx) > canvasHeight;
-
- if (lastWidthPartHeight)
- {
- int widthsAbove = Math.max(0, visibleWidths - 2);
- int ypos = wrappedRepeatHeightPx * widthsAbove
- + wrappedSpaceAboveAlignment;
- int endRes = ranges.getEndRes();
- endRes += widthsAbove * viewportWidth;
- int startRes = endRes - columns;
- int xOffset = ((startRes - ranges.getStartRes()) % viewportWidth)
- * charWidth;
-
- /*
- * white fill first to erase annotations
- */
- gg.translate(xOffset, 0);
- gg.setColor(Color.white);
- gg.fillRect(labelWidthWest, ypos,
- (endRes - startRes + 1) * charWidth, wrappedRepeatHeightPx);
- gg.translate(-xOffset, 0);
-
- drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight);
- }
-
- /*
- * draw newly visible columns in last wrapped width (none if we
- * have reached the end of the alignment)
- * y-offset for drawing last width is height of widths above,
- * plus one gap row
- */
- int widthsAbove = visibleWidths - 1;
- int ypos = wrappedRepeatHeightPx * widthsAbove
- + wrappedSpaceAboveAlignment;
- int endRes = ranges.getEndRes();
- endRes += widthsAbove * viewportWidth;
- int startRes = endRes - columns + 1;
-
- /*
- * white fill first to erase annotations
- */
- int xOffset = ((startRes - ranges.getStartRes()) % viewportWidth)
- * charWidth;
- gg.translate(xOffset, 0);
- gg.setColor(Color.white);
- int width = viewportWidth * charWidth - xOffset;
- gg.fillRect(labelWidthWest, ypos, width, wrappedRepeatHeightPx);
- gg.translate(-xOffset, 0);
-
- gg.setFont(av.getFont());
- gg.setColor(Color.black);
-
- if (startRes < ranges.getVisibleAlignmentWidth())
- {
- drawWrappedWidth(gg, ypos, startRes, endRes, canvasHeight);
- }
-
- /*
- * and finally, white fill any space below the visible alignment
- */
- int heightBelow = canvasHeight - visibleWidths * wrappedRepeatHeightPx;
- if (heightBelow > 0)
- {
- gg.setColor(Color.white);
- gg.fillRect(0, canvasHeight - heightBelow, getWidth(), heightBelow);
- }
- }
-
- /**
- * Shifts the visible alignment by the specified number of columns - left if
- * negative, right if positive. Copies and moves sequences and annotations (if
- * shown). Scales, hidden column markers and any newly visible columns must be
- * drawn separately.
- *
- * @param positions
- */
- protected void shiftWrappedAlignment(int positions)
- {
- if (positions == 0)
- {
- return;
- }
- int charWidth = av.getCharWidth();
-
- int canvasHeight = getHeight();
- ViewportRanges ranges = av.getRanges();
- int viewportWidth = ranges.getViewportWidth();
- int widthToCopy = (ranges.getViewportWidth() - Math.abs(positions))
- * charWidth;
- int heightToCopy = wrappedRepeatHeightPx - wrappedSpaceAboveAlignment;
- int xMax = ranges.getVisibleAlignmentWidth();
-
- if (positions > 0)
- {
- /*
- * shift right (after scroll left)
- * for each wrapped width (starting with the last), copy (width-positions)
- * columns from the left margin to the right margin, and copy positions
- * columns from the right margin of the row above (if any) to the
- * left margin of the current row
- */
-
- /*
- * get y-offset of last wrapped width, first row of sequences
- */
- int y = canvasHeight / wrappedRepeatHeightPx * wrappedRepeatHeightPx;
- y += wrappedSpaceAboveAlignment;
- int copyFromLeftStart = labelWidthWest;
- int copyFromRightStart = copyFromLeftStart + widthToCopy;
-
- while (y >= 0)
+ else if (eventName.equals(ViewportRanges.STARTSEQ))
{
- gg.copyArea(copyFromLeftStart, y, widthToCopy, heightToCopy,
- positions * charWidth, 0);
- if (y > 0)
- {
- gg.copyArea(copyFromRightStart, y - wrappedRepeatHeightPx,
- positions * charWidth, heightToCopy, -widthToCopy,
- wrappedRepeatHeightPx);
- }
-
- y -= wrappedRepeatHeightPx;
+ // scroll
+ fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
}
- }
- else
- {
- /*
- * shift left (after scroll right)
- * for each wrapped width (starting with the first), copy (width-positions)
- * columns from the right margin to the left margin, and copy positions
- * columns from the left margin of the row below (if any) to the
- * right margin of the current row
- */
- int xpos = av.getRanges().getStartRes();
- int y = wrappedSpaceAboveAlignment;
- int copyFromRightStart = labelWidthWest - positions * charWidth;
-
- while (y < canvasHeight)
+ else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
{
- gg.copyArea(copyFromRightStart, y, widthToCopy, heightToCopy,
- positions * charWidth, 0);
- if (y + wrappedRepeatHeightPx < canvasHeight - wrappedRepeatHeightPx
- && (xpos + viewportWidth <= xMax))
- {
- gg.copyArea(labelWidthWest, y + wrappedRepeatHeightPx, -positions
- * charWidth, heightToCopy, widthToCopy,
- -wrappedRepeatHeightPx);
- }
-
- y += wrappedRepeatHeightPx;
- xpos += viewportWidth;
+ fastPaint(scrollX, ((int[]) evt.getNewValue())[1]
+ - ((int[]) evt.getOldValue())[1]);
}
}
}
-
/**
* Redraws any positions in the search results in the visible region of a
* wrapped alignment. Any highlights are drawn depending on the search results
{
return false;
}
- int charHeight = av.getCharHeight();
-
+
boolean matchFound = false;
- calculateWrappedGeometry(getWidth(), getHeight());
int wrappedWidth = av.getWrappedWidth();
- int wrappedHeight = wrappedRepeatHeightPx;
+ int wrappedHeight = getRepeatHeightWrapped();
ViewportRanges ranges = av.getRanges();
int canvasHeight = getHeight();
}
/**
+ * Answers the height in pixels of a repeating section of the wrapped
+ * alignment, including space above, scale above if shown, sequences, and
+ * annotation panel if shown
+ *
+ * @return
+ */
+ protected int getRepeatHeightWrapped()
+ {
+ // gap (and maybe scale) above
+ int repeatHeight = charHeight * (av.getScaleAboveWrapped() ? 2 : 1);
+
+ // add sequences
+ repeatHeight += av.getRanges().getViewportHeight() * charHeight;
+
+ // add annotations panel height if shown
+ repeatHeight += getAnnotationHeight();
+
+ return repeatHeight;
+ }
+
+ /**
* Answers the width in pixels of the left scale labels (0 if not shown)
*
* @return
git://source.jalview.org / jalview.git / commitdiff